Bacteriorhodopsin (bR) is a transmembrane protein that functions as a light-driven proton pump in the cell membrane of Halobacterium salinarium. The function is achieved through a cyclic process initiated by the absorption of a photon [34]. The pump cycle is characterized by a series of intermediates that differ both spectroscopically and structurally. Water molecules near the chromophore of bR are experimentally known to play an important role in the function of the protein. Recently, a better resolved structure of bR has been reported [47], yet the position of the water molecules is still not well-defined. Our work* aims at placing the water molecules in the new structure according to thermodynamic criteria [74]. The free energy of solvation is calculated, and the probability of occupation of cavities in the proton channel by one (or more) water molecule(s) is calculated. Our simulations indicate that in the new structure, a water molecule located near the Schiff Base, on the extracellular side is very stable, while a water molecule on the cytoplasmic side is less stable. These results differ from the ones obtained using the previous structure [74]. We plan to continue this work and explore other possible hydration sites. The resulting model will be used for quantum mechanical simulations of the primary photo-event.